PDB-7q17: Beta-lactoglobulin mutant FAW (I56F/L39A/M107W), unliganded form

ID or keywords:

Entry

Database: PDB / ID: 7q17

Title

Beta-lactoglobulin mutant FAW (I56F/L39A/M107W), unliganded form

Components

Beta-lactoglobulin

Keywords

TRANSPORT PROTEIN / lactoglobulin / mutation / desipramine

Function / homology

Function and homology information

retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Loch, J.I. / Barciszewski, J. / Lewinski, K.

Funding support

1items

Citation

Journal: Iucrj / Year: 2022
Title: New ligand-binding sites identified in the crystal structures of [beta]-lactoglobulin complexes with desipramine
Authors: Loch, J.I. / Barciszewski, J. / Sliwiak, J. / Bonarek, P. / Wrobel, P. / Pokrywka, K. / Shabalin, I.G. / Minor, W. / Jaskolski, M. / Lewinski, K.

History

Deposition	Oct 18, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 11, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7q17.cif.gz	75.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7q17.ent.gz		Display	PDB format
PDBx/mmJSON format	7q17.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7q17_validation.pdf.gz	432.1 KB	Display	wwPDB validaton report
Full document	7q17_full_validation.pdf.gz	432.4 KB	Display
Data in XML	7q17_validation.xml.gz	9.1 KB	Display
Data in CIF	7q17_validation.cif.gz	11.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/7q17 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/7q17	HTTPS FTP

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Related structure data

Related structure data	7q18C 7q19C 7q2nC 7q2oC 7q2pC 1bsyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (5) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

AAA: Beta-lactoglobulin

hetero molecules

18.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Beta-lactoglobulin

hetero molecules

AAA: Beta-lactoglobulin

hetero molecules

defined by author
Evidence: gel filtration
36.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.083, 53.083, 111.469
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	AAA-305- HOH

#1: Protein	Beta-lactoglobulin / Beta-LG Mass: 18279.965 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39A, I56F, M107W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P02754
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.40 M ammonium sulfate, 0.5 M Tris-HCl pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 23, 2019
Radiation	Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.8→45.97 Å / Num. obs: 17450 / % possible obs: 99.8 % / Redundancy: 4.31 % / CC_1/2: 0.999 / R_rim(I) all: 0.057 / Net I/σ(I): 13.73
Reflection shell	Resolution: 1.8→1.91 Å / Redundancy: 4.02 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2615 / CC_1/2: 0.59 / R_rim(I) all: 0.972 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy

Resolution: 1.8→45.971 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.952 / WR_factor R_free: 0.239 / WR_factor R_work: 0.19 / SU B: 5.814 / SU ML: 0.087 / Average fsc free: 0.9138 / Average fsc work: 0.9327 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2264	1000	5.731 %
R_work	0.183	16448	-
all	0.185	-	-
obs	-	17448	99.652 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 40.063 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.125 Å²	0.062 Å²	-0 Å²
2-	-	0.125 Å²	0 Å²
3-	-	-	-0.405 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→45.971 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1251	0	4	98	1353

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1278
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1245
X-RAY DIFFRACTION	r_angle_refined_deg	1.619	1.641	1729
X-RAY DIFFRACTION	r_angle_other_deg	1.317	1.583	2886
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.357	5	156
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.44	25.517	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.242	15	239
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.308	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	170
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1411
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	255
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	213
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	1081
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	589
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	601
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.052	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.239	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.277	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.199	0.2	10
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.052	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.318	3.384	630
X-RAY DIFFRACTION	r_mcbond_other	2.308	3.382	629
X-RAY DIFFRACTION	r_mcangle_it	3.425	5.049	784
X-RAY DIFFRACTION	r_mcangle_other	3.424	5.051	785
X-RAY DIFFRACTION	r_scbond_it	3.159	3.817	647
X-RAY DIFFRACTION	r_scbond_other	3.157	3.82	648
X-RAY DIFFRACTION	r_scangle_it	5.064	5.541	944
X-RAY DIFFRACTION	r_scangle_other	5.061	5.544	945
X-RAY DIFFRACTION	r_lrange_it	7.002	40.087	1358
X-RAY DIFFRACTION	r_lrange_other	7.002	39.765	1344

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.313	72	0.289	1192	0.291	1281	0.801	0.826	98.6729	0.288
1.847-1.897	0.286	71	0.257	1162	0.259	1239	0.864	0.877	99.5157	0.248
1.897-1.952	0.258	68	0.218	1124	0.22	1192	0.91	0.917	100	0.199
1.952-2.012	0.276	67	0.191	1098	0.196	1165	0.899	0.936	100	0.167
2.012-2.078	0.267	64	0.19	1049	0.194	1113	0.908	0.939	100	0.166
2.078-2.151	0.23	63	0.189	1047	0.191	1110	0.922	0.937	100	0.166
2.151-2.232	0.257	62	0.194	1015	0.198	1078	0.919	0.937	99.9072	0.166
2.232-2.323	0.235	59	0.191	969	0.193	1029	0.938	0.947	99.9028	0.163
2.323-2.426	0.24	57	0.171	935	0.175	992	0.936	0.957	100	0.146
2.426-2.544	0.252	53	0.177	875	0.181	928	0.922	0.953	100	0.154
2.544-2.681	0.207	51	0.178	842	0.18	901	0.939	0.952	99.1121	0.161
2.681-2.843	0.222	49	0.206	799	0.207	852	0.933	0.94	99.5305	0.194
2.843-3.039	0.277	47	0.204	771	0.208	818	0.902	0.935	100	0.198
3.039-3.281	0.303	43	0.189	717	0.196	760	0.904	0.951	100	0.19
3.281-3.592	0.168	40	0.183	662	0.182	702	0.964	0.964	100	0.188
3.592-4.013	0.163	37	0.163	603	0.163	640	0.976	0.97	100	0.184
4.013-4.628	0.233	32	0.147	532	0.152	567	0.949	0.972	99.4709	0.182
4.628-5.654	0.222	28	0.147	455	0.151	489	0.943	0.973	98.773	0.181
5.654-7.936	0.226	23	0.215	374	0.215	401	0.958	0.954	99.0025	0.255
7.936-45.971	0.149	14	0.201	227	0.198	252	0.968	0.964	95.6349	0.281

Refinement TLS params.

Method: refined / Origin x: -15.1268 Å / Origin y: 4.2842 Å / Origin z: 3.3141 Å

	11	12	13	21	22	23	31	32	33
T	0.0466 Å²	-0.0245 Å²	-0.0032 Å²	-	0.0368 Å²	0.0131 Å²	-	-	0.0098 Å²
L	0.0977 °²	-0.0134 °²	0.2655 °²	-	0.9645 °²	0.3476 °²	-	-	1.7266 °²
S	-0.046 Å °	0.0474 Å °	0.0127 Å °	-0.0039 Å °	-0.0216 Å °	0.0505 Å °	0.0232 Å °	0.0995 Å °	0.0676 Å °

Refinement TLS group

Selection: ALL

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